..........................                                      
 ooooooooooooooooooooooooooooo        CURRENT SETTINGS        ooooooooooooooooooooooooooooooooooo
                                 ..........................                                      

                . Sequence filename : 				 proteic_M1372_23x394_2003.phy
                . Data type :             			 aa
                . Sequence format : 				 interleaved
                . Number of data sets : 			 1
                . Nb of bootstrapped data sets : 		 0
                . Model name : 					 WAG
                . Proportion of invariable sites :		 0.000000
                . Number of subst. rate categs : 		 4
                . Gamma distribution parameter : 		 estimated
                . 'Middle' of each rate class  : 		 mean
                . Amino acid equilibrium frequencies : 		 model
                . Optimise tree topology : 			 yes
                . Tree topology search : 			 SPRs
                . Starting tree : 				 BioNJ
                . Add random input tree : 			 no
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. 3 sites are made from completely undetermined states ('X', '-', '?')...

. Compressing sequences...

. 246 patterns found. (out of a total of 394 sites) 

. 162 sites without polymorphism (41.12%).

. Computing pairwise distances...

. Building BioNJ tree...

. This analysis requires at least 13Mo of memory space.

. Maximizing likelihood (using SPR moves)...

. (    0 sec) [     -4512.1912] [Alpha              ][  0.596203]
. (    1 sec) [     -4510.7574] [  648] [depth=    2]
. (    2 sec) [     -4509.8214] [  651] [depth=    1]
. (    4 sec) [     -4507.5758] [  648] [depth=    1]
. (    4 sec) [     -4504.4834] [  648] [depth=    2]
. (    4 sec) [     -4494.0203] [  645] [depth=    5]
. (    4 sec) [     -4493.9133] [  646] [depth=    1]
. (    4 sec) [     -4493.5419] [  643] [depth=    4]
. (    5 sec) [     -4492.5401] [  643] [depth=    1]
. (    5 sec) [     -4492.0982] [  643] [depth=    1]
. (    5 sec) [     -4491.8533] [  643] [depth=    1]
. (    5 sec) [     -4491.6218] [  643] [depth=    1]
. (    6 sec) [     -4490.2200] [  643] [depth=    1]
. (    7 sec) [     -4490.1385] [  643] [depth=    1]
. (    7 sec) [     -4489.9858] [  643] [depth=    1]
. (    7 sec) [     -4488.6072] [  643] [depth=    1]
. (    9 sec) [     -4487.6593] [  644] [depth=    2]
. (    9 sec) [     -4478.2792] [Branch lengths     ]
. (    9 sec) [     -4477.9239] [Alpha              ][  0.655814]
. (   10 sec) [     -4474.8195] [  646] [depth=    2]
. (   13 sec) [     -4472.3468] [  646] [depth=    8]
. (   14 sec) [     -4470.5793] [  645] [depth=    1]
. (   14 sec) [     -4466.4536] [  644] [depth=    1]
. (   18 sec) [     -4464.2191] [Branch lengths     ]
. (   18 sec) [     -4464.2130] [Alpha              ][  0.664331]
. (   21 sec) [     -4463.5828] [  645] [depth=    8]
. (   22 sec) [     -4463.4729] [  645] [depth=    1]
. (   22 sec) [     -4463.3230] [  645] [depth=    1]
. (   25 sec) [     -4463.3008] [  645] [depth=    1]
. (   27 sec) [     -4461.8982] [Branch lengths     ]
. (   27 sec) [     -4461.8980] [Alpha              ][  0.665862]
. (   36 sec) [     -4461.8595] [Branch lengths     ]
. (   36 sec) [     -4461.8595] [Topology           ]
. (   38 sec) [     -4461.8586] [Topology           ]
. (   38 sec) [     -4461.8586] [Alpha              ][  0.665862]

. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -4461.858646.

. Printing the most likely tree in file 'proteic_M1372_23x394_2003.phy_phyml_tree.txt'...


. Time used 0h0m47s

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
45.75user 0.00system 0:47.37elapsed 96%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (0major+0minor)pagefaults 0swaps